Ship kseqpp headers with the project.

CMakeLists.txt

@@ -123,10 +123,14 @@ else()
 endif()
 
 ## Check dependencies and download them if not found
-## BitMagic - supplied with the project
+### BitMagic - supplied with the project
 set(CMAKE_BITMAGIC_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/external/BitMagic-7.12.3/src)
 include_directories(${CMAKE_BITMAGIC_HEADERS})
 
+### kseq++
+set(CMAKE_KSEQPP_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/external/kseqpp-1.1.2/include)
+include_directories(${CMAKE_KSEQPP_HEADERS})
+
 ## bxzstr
 if (DEFINED CMAKE_BXZSTR_HEADERS)
   message(STATUS "bxzstr headers provided in: ${CMAKE_BXZSTR_HEADERS}")
@@ -169,25 +173,6 @@ else()
 endif()
 include_directories("${CMAKE_CXXARGS_HEADERS}")
 
-## kseqpp
-if (DEFINED CMAKE_KSEQPP_HEADERS)
-  message(STATUS "kseq++ headers provided in: ${CMAKE_KSEQPP_HEADERS}")
-else()
-  FetchContent_Declare(kseqpp
-    GIT_REPOSITORY    https://github.com/cartoonist/kseqpp
-    GIT_TAG           v1.1.2
-    PREFIX            "external"
-    SOURCE_DIR        "${CMAKE_CURRENT_SOURCE_DIR}/external/kseqpp"
-    BUILD_IN_SOURCE   0
-    BUILD_COMMAND     ""
-    CONFIGURE_COMMAND ""
-    INSTALL_COMMAND   ""
-    )
-  FetchContent_MakeAvailable(kseqpp)
-  set(CMAKE_KSEQPP_HEADERS ${CMAKE_CURRENT_SOURCE_DIR}/external/kseqpp/include)
-endif()
-include_directories("${CMAKE_KSEQPP_HEADERS}")
-
 # Link libraries
 if (OPENMP_FOUND)
   target_link_libraries(libalignmentwriter OpenMP::OpenMP_CXX)

external/kseqpp-1.1.2/CMakeLists.txt

@@ -0,0 +1,86 @@
+cmake_minimum_required(VERSION 3.10)
+project(kseq++ VERSION 1.1.2 LANGUAGES CXX)
+
+#options
+option(BUILD_TESTING "Build test programs" OFF)  # ignored by default
+option(BUILD_BENCHMARKING "Build benchmark program" OFF)  # ignored by default
+
+# Include external modules
+include(GNUInstallDirs)
+include(CMakePackageConfigHelpers)
+
+# Finding dependencies.
+find_package(ZLIB REQUIRED)
+find_package(BZip2 REQUIRED)
+find_package(Threads REQUIRED)
+
+# Creating an INTERFACE library
+add_library(kseq++ INTERFACE)
+# Defining include directories
+target_include_directories(kseq++
+  INTERFACE $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>;$<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
+  INTERFACE $<TARGET_PROPERTY:ZLIB::ZLIB,INTERFACE_INCLUDE_DIRECTORIES>
+  INTERFACE $<TARGET_PROPERTY:BZip2::BZip2,INTERFACE_INCLUDE_DIRECTORIES>
+  INTERFACE $<TARGET_PROPERTY:Threads::Threads,INTERFACE_INCLUDE_DIRECTORIES>)
+# Defining link libraries
+target_link_libraries(kseq++
+  INTERFACE $<BUILD_INTERFACE:ZLIB::ZLIB>;$<INSTALL_INTERFACE:ZLIB::ZLIB>
+  INTERFACE $<BUILD_INTERFACE:BZip2::BZip2>;$<INSTALL_INTERFACE:BZip2::BZip2>
+  INTERFACE $<BUILD_INTERFACE:Threads::Threads>;$<INSTALL_INTERFACE:Threads::Threads>)
+# Use C++17
+target_compile_features(kseq++ INTERFACE cxx_std_11)
+# Generating the configure header file
+configure_file(include/kseq++/config.hpp.in ${PROJECT_SOURCE_DIR}/include/kseq++/config.hpp @ONLY)
+# Generating pkgconfig file
+configure_file(kseq++.pc.in ${PROJECT_SOURCE_DIR}/kseq++.pc @ONLY)
+# Setting header files
+file(GLOB HEADER_FILES RELATIVE "${PROJECT_SOURCE_DIR}/include" "${PROJECT_SOURCE_DIR}/include/kseq++/*.h")
+list(TRANSFORM HEADER_FILES PREPEND "${PROJECT_SOURCE_DIR}/include/" OUTPUT_VARIABLE BUILD_HEADER_FILES)
+list(TRANSFORM HEADER_FILES PREPEND "${CMAKE_INSTALL_FULL_INCLUDEDIR}/" OUTPUT_VARIABLE INSTALL_HEADER_FILES)
+# Defining target sources
+target_sources(kseq++
+  INTERFACE "$<BUILD_INTERFACE:${BUILD_HEADER_FILES}>;$<INSTALL_INTERFACE:${INSTALL_HEADER_FILES}>")
+# Defining `kseq++::kseq++` alias
+add_library(kseq++::kseq++ ALIAS kseq++)
+# Install targets
+install(DIRECTORY include/kseq++ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} PATTERN "*.hpp.in" EXCLUDE)
+install(FILES kseq++.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+# Exporting targets
+install(TARGETS kseq++ EXPORT kseq++-targets)
+install(EXPORT kseq++-targets NAMESPACE kseq++:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/kseq++)
+# Creating the package configuration file
+configure_package_config_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/kseq++-config.cmake.in
+  "${CMAKE_CURRENT_BINARY_DIR}/kseq++-config.cmake"
+  INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/kseq++)
+# Generating the version file for the configuration file
+write_basic_package_version_file(
+  "${CMAKE_CURRENT_BINARY_DIR}/kseq++-config-version.cmake"
+  VERSION "${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR}.${PROJECT_VERSION_PATCH}"
+  COMPATIBILITY AnyNewerVersion)
+# Install generated configuration files
+install(FILES "${CMAKE_CURRENT_BINARY_DIR}/kseq++-config.cmake"
+  "${CMAKE_CURRENT_BINARY_DIR}/kseq++-config-version.cmake"
+  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/kseq++)
+
+# Adding test submodule
+if(BUILD_TESTING)
+  add_subdirectory(test)
+endif(BUILD_TESTING)
+
+# Adding benchmark submodule
+if(BUILD_BENCHMARKING)
+  add_subdirectory(benchmark)
+endif(BUILD_BENCHMARKING)
+
+# Packaging configuration
+set(CPACK_PACKAGE_NAME "kseqpp")
+set(CPACK_PACKAGE_VENDOR "cartoonist")
+set(CPACK_GENERATOR "STGZ;TGZ;RPM")
+set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)")
+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
+set(CPACK_SYSTEM_NAME "noarch")
+set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
+set(CPACK_RESOURCE_FILE_README "${CMAKE_CURRENT_SOURCE_DIR}/README.md")
+include(CPack)

external/kseqpp-1.1.2/KSEQ_LICENSE

@@ -0,0 +1,23 @@
+The MIT License
+
+Copyright (c) 2008, 2009, 2011 Attractive Chaos <[email protected]>
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

external/kseqpp-1.1.2/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Ali Ghaffaari
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.